[gmx-users] Re: amber force field in Gromacs
Hi Alan, Thank you for all your efforts. This is getting strange, I tried following your procedure below but is still does not work for me: step 3500, will finish Fri Dec 4 09:56:51 2009Warning: 1-4 interaction between 6 and 10 at distance 1.454 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size kind regards, Servaas Message: 1 Date: Thu, 3 Dec 2009 11:23:14 + From: Alan alanwil...@gmail.com Subject: [gmx-users] Re: amber force field in Gromacs To: gmx-users@gromacs.org Message-ID: cf58c8d00912030323v97c0556oa6aa1942c4625...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Dear Servaas, Tested again in 'vacuum' and I saw no problems. Here goes what I did: #-- cat EOF | leap.in verbosity 1 source leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm ad da_amber.top da_amber.crd savepdb ad DA.pdb quit EOF tleap -f leap.in | leap.out acpypi -x da_amber.crd -p da_amber.top -d # acpypi generates em.mdp and md.mdp cat EOF | md.mdp cpp = /usr/bin/cpp define = ;-DFLEXIBLE integrator = md nsteps = 25 constraints = none emtol= 1000.0 emstep = 0.01 comm_mode= angular ns_type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 100 pbc = no EOF editconf -bt cubic -d 1.0 -f da_amber_GMX.gro -o da_amber_GMX.gro #Single precision grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr #-- As you may suspect from the beginning it may be something in your mdp file. Case the example above works, I would suggest you to try the mdp for solvent box I sent before in a long simulation. Good luck. Regards, Alan On Wed, Dec 2, 2009 at 11:10, Alan alanwil...@gmail.com wrote: Dear Servaas, In tleap did you really did: TLEAP tleap -f leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm da da_amber.top da_amber.crd If so, it's wrong, it should be: saveamberparm ad da_amber.top da_amber.crd ^^^ and not 'da' Besides, I tried to reproduce what you did using what I think would be fine and... everything went fine! Energies after minimisation in single and double were almost identical and trajectories diverted normally. Please check what I did. # begin commands cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist= 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = grid rlist= 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF cat EOF | leap.in verbosity 1 source leaprc.ff99SB ad = sequence { DA5 DA DA3 } solvatebox ad TIP3PBOX 10.0 addions ad Na+ 5 addions ad Cl- 3 saveamberparm ad da_amber.top da_amber.crd savepdb ad DA.pdb quit EOF tleap -f leap.in | leap.out acpypi -x
[gmx-users] Re: amber force field in Gromacs
Dear Servaas, Tested again in 'vacuum' and I saw no problems. Here goes what I did: #-- cat EOF | leap.in verbosity 1 source leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm ad da_amber.top da_amber.crd savepdb ad DA.pdb quit EOF tleap -f leap.in | leap.out acpypi -x da_amber.crd -p da_amber.top -d # acpypi generates em.mdp and md.mdp cat EOF | md.mdp cpp = /usr/bin/cpp define = ;-DFLEXIBLE integrator = md nsteps = 25 constraints = none emtol= 1000.0 emstep = 0.01 comm_mode= angular ns_type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 100 pbc = no EOF editconf -bt cubic -d 1.0 -f da_amber_GMX.gro -o da_amber_GMX.gro #Single precision grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr #-- As you may suspect from the beginning it may be something in your mdp file. Case the example above works, I would suggest you to try the mdp for solvent box I sent before in a long simulation. Good luck. Regards, Alan On Wed, Dec 2, 2009 at 11:10, Alan alanwil...@gmail.com wrote: Dear Servaas, In tleap did you really did: TLEAP tleap -f leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm da da_amber.top da_amber.crd If so, it's wrong, it should be: saveamberparm ad da_amber.top da_amber.crd ^^^ and not 'da' Besides, I tried to reproduce what you did using what I think would be fine and... everything went fine! Energies after minimisation in single and double were almost identical and trajectories diverted normally. Please check what I did. # begin commands cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist= 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = grid rlist= 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF cat EOF | leap.in verbosity 1 source leaprc.ff99SB ad = sequence { DA5 DA DA3 } solvatebox ad TIP3PBOX 10.0 addions ad Na+ 5 addions ad Cl- 3 saveamberparm ad da_amber.top da_amber.crd savepdb ad DA.pdb quit EOF tleap -f leap.in | leap.out acpypi -x da_amber.crd -p da_amber.top -d #Single precision grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun -v -deffnm em #Polak-Ribiere Conjugate Gradients converged to Fmax 1000 in 22 steps #Potential Energy = -6.2280516e+04 #Maximum force = 7.5868494e+02 on atom 98 #Norm of force = 1.0447179e+02 grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun -v -deffnm md #Double precision grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun_d -v -deffnm em #Polak-Ribiere Conjugate Gradients converged to Fmax 1000 in 22 steps #Potential Energy = -6.22813514022256e+04 #Maximum force = 7.58238100790309e+02 on atom 98 #Norm of force = 1.04358667410458e+02 grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun_d -v -deffnm md # end commands Regards, Alan On Tue, Dec 1, 2009 at 13:56, Alan alanwil...@gmail.com wrote: Dear Servaas, I've been following
[gmx-users] Re: amber force field in Gromacs
Dear Servaas, In tleap did you really did: TLEAP tleap -f leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm da da_amber.top da_amber.crd If so, it's wrong, it should be: saveamberparm ad da_amber.top da_amber.crd ^^^ and not 'da' Besides, I tried to reproduce what you did using what I think would be fine and... everything went fine! Energies after minimisation in single and double were almost identical and trajectories diverted normally. Please check what I did. # begin commands cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist= 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = grid rlist= 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF cat EOF | leap.in verbosity 1 source leaprc.ff99SB ad = sequence { DA5 DA DA3 } solvatebox ad TIP3PBOX 10.0 addions ad Na+ 5 addions ad Cl- 3 saveamberparm ad da_amber.top da_amber.crd savepdb ad DA.pdb quit EOF tleap -f leap.in | leap.out acpypi -x da_amber.crd -p da_amber.top -d #Single precision grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun -v -deffnm em #Polak-Ribiere Conjugate Gradients converged to Fmax 1000 in 22 steps #Potential Energy = -6.2280516e+04 #Maximum force = 7.5868494e+02 on atom 98 #Norm of force = 1.0447179e+02 grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun -v -deffnm md #Double precision grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun_d -v -deffnm em #Polak-Ribiere Conjugate Gradients converged to Fmax 1000 in 22 steps #Potential Energy = -6.22813514022256e+04 #Maximum force = 7.58238100790309e+02 on atom 98 #Norm of force = 1.04358667410458e+02 grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun_d -v -deffnm md # end commands Regards, Alan On Tue, Dec 1, 2009 at 13:56, Alan alanwil...@gmail.com wrote: Dear Servaas, I've been following your thread. I am the developer of acpypi and thanks for giving a try. So, as you may already know, you are trying acpypi as amb2gmx.pl so far, but you also seemed to have read acpypi wikis and realise that acpypi can help you to generate the whole topology for a ligand. However, AFAIU you have only regular NA and not modified ones neither ligands, right? But then why are you using RED? I understand your approach about using tleap to create your whole system and then convert it to GMX. It should work at first but it is clearly not as you reported. So, here goes some of my recommendations: 1) GMX is vacuum is unrealistic and prone for errors. There's no GB implementation as far as I know. 2) Have you try to use pdb2gmx to generate your files from your pdb directly to GMX? 3) When you say that gmx double precision works, is your system in vacuum or with solvent? 4) if using tleap, create your system with solvent and ions and then use acpypi to convert to gmx. The use of amb2gmx or acpypi is to give you a system to be run immediately in gromacs doing just a grompp and mdrun. Using editconf will change the parameters of your box and it may have serious implications besides that in amber we don't have dodecahedron, so if doing what you're doing then you're not replicating the conditions you have in amber with those in gmx (although it puzzles me that gmx double works, with the commands you gave in gmx?). I would ask you to give more details and even a detailed step by step of commands of what you're doing including tleap. Regards, Alan On Tue, Dec 1, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote:
[gmx-users] Re: amber force field in Gromacs
Dear Servaas, In tleap did you really did: TLEAP tleap -f leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm da da_amber.top da_amber.crd If so, it's wrong, it should be: saveamberparm ad da_amber.top da_amber.crd ^^^ and not 'da' Yes of course just a typo here Besides, I tried to reproduce what you did using what I think would be fine and... everything went fine! Energies after minimisation in single and double were almost identical and trajectories diverted normally. Did you also try running it in vacuum? In solvent the problems occur only after a large number of steps. In vacuum they occur very fast. I know vacuum is not the way to go, but I consider it as quick test, if a short simulation in vacuum gives strange things it is an indication of a problem with the parameters (force fiels or others...). Amber doesn't give me any problems in vacuum, this gives me an indication that the vacuum is not the problem here. Please check what I did. # begin commands cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist= 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = grid rlist= 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF cat EOF | leap.in verbosity 1 source leaprc.ff99SB ad = sequence { DA5 DA DA3 } solvatebox ad TIP3PBOX 10.0 addions ad Na+ 5 addions ad Cl- 3 saveamberparm ad da_amber.top da_amber.crd savepdb ad DA.pdb quit EOF tleap -f leap.in | leap.out acpypi -x da_amber.crd -p da_amber.top -d #Single precision grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun -v -deffnm em #Polak-Ribiere Conjugate Gradients converged to Fmax 1000 in 22 steps #Potential Energy = -6.2280516e+04 #Maximum force = 7.5868494e+02 on atom 98 #Norm of force = 1.0447179e+02 grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun -v -deffnm md #Double precision grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr mdrun_d -v -deffnm em #Polak-Ribiere Conjugate Gradients converged to Fmax 1000 in 22 steps #Potential Energy = -6.22813514022256e+04 #Maximum force = 7.58238100790309e+02 on atom 98 #Norm of force = 1.04358667410458e+02 grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr mdrun_d -v -deffnm md # end commands Regards, Alan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: amber force field in Gromacs
Message: 6 Date: Tue, 01 Dec 2009 07:38:29 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] amber force field in Gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b142d45.5050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed servaas wrote: Hello, I tried using the amber force field in GROMACS. I proceeded as follows: Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine. When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent): integrator = md dt = 0.002 nsteps = 25 nstcomm = 1 ;output nstxout = 1 nstvout = 1 nstfout = 0 nstlog= 500 nstenergy = 1 nstlist = 10 ns_type = grid rlist= 1.2 coulombtype = PME rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.2 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-5 ;constraints constraints = all-bonds ; temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps = system ref_t = 300 pcoupl = no I get LINCS errors and eventually a crash. Now I tried running the same simulation with the same force field parameters in amber and everything was fine. I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here) that I created in tleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'. The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions? Strange also that double precision seems to work just fine When switching precision, are the starting configurations different? What are the actual command lines in your procedures? It is the exact same structure, when I look at the trajectory I see the O3'-H rotate towards the O4' in the single precision trajectory they come too close and clash. In the double precision trajectory the O3'-H also rotates towards O4' but they do not come so close... I did not include the command lines for amber and RED, please let me know if they are relevant to you. So first I use RED to determine the charges of different fragments of my molecule. The result are several mol2 files, I use tleap to combine this mol2 file with parts of existing amber fragments. I save an amber top and amber crd file. I convert this with amb2gmx or with acpypi (tried both same result in the simulation). ./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro or python acpypi.py -x ad_test.crd -p ad_test.top -o gmx -b gro Then I add a box in gromacs: editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro I run a minimization: grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr mdrun -deffnm em (Also tried putting a position restraint step in between, did not resolve the problem) grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr mdrun -deffnm md Extra remarks: Simulation in vacuum is not realistic and the FF is not made for this but I also tried running it with counter ions and water, same result. In amber I can simulate the exact same molecule in vacuum, with same parameters without any problems. The exact same problem occurs if I start with a small natural nucleic acid sequence (3*DA), so 100% amber FF parameters (but created in amber and converted with amb2gmx.pl). Kind regards, Servaas Mark -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 67, Issue 152 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: amber force field in Gromacs
Hi, Vacuum simulations are trickier than in solvent, more often causing lincs errors. Have you tried playing around with lincs order and lincs iter? /Erik servaas skrev: Message: 6 Date: Tue, 01 Dec 2009 07:38:29 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] amber force field in Gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b142d45.5050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed servaas wrote: Hello, I tried using the amber force field in GROMACS. I proceeded as follows: Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine. When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent): integrator = md dt = 0.002 nsteps = 25 nstcomm = 1 ;output nstxout = 1 nstvout = 1 nstfout = 0 nstlog= 500 nstenergy = 1 nstlist = 10 ns_type = grid rlist= 1.2 coulombtype = PME rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.2 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-5 ;constraints constraints = all-bonds ; temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps = system ref_t = 300 pcoupl = no I get LINCS errors and eventually a crash. Now I tried running the same simulation with the same force field parameters in amber and everything was fine. I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here) that I created in tleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'. The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions? Strange also that double precision seems to work just fine When switching precision, are the starting configurations different? What are the actual command lines in your procedures? It is the exact same structure, when I look at the trajectory I see the O3'-H rotate towards the O4' in the single precision trajectory they come too close and clash. In the double precision trajectory the O3'-H also rotates towards O4' but they do not come so close... I did not include the command lines for amber and RED, please let me know if they are relevant to you. So first I use RED to determine the charges of different fragments of my molecule. The result are several mol2 files, I use tleap to combine this mol2 file with parts of existing amber fragments. I save an amber top and amber crd file. I convert this with amb2gmx or with acpypi (tried both same result in the simulation). ./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro or python acpypi.py -x ad_test.crd -p ad_test.top -o gmx -b gro Then I add a box in gromacs: editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro I run a minimization: grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr mdrun -deffnm em (Also tried putting a position restraint step in between, did not resolve the problem) grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr mdrun -deffnm md Extra remarks: Simulation in vacuum is not realistic and the FF is not made for this but I also tried running it with counter ions and water, same result. In amber I can simulate the exact same molecule in vacuum, with same parameters without any problems. The exact same problem occurs if I start with a small natural nucleic acid sequence (3*DA), so 100% amber FF parameters (but created in amber and converted with amb2gmx.pl). Kind regards, Servaas Mark -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 67, Issue 152 ** -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www
[gmx-users] Re: amber force field in Gromacs
-- Message: 4 Date: Tue, 01 Dec 2009 10:51:17 +0100 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] Re: amber force field in Gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b14e715.3030...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, Vacuum simulations are trickier than in solvent, more often causing lincs errors. Have you tried playing around with lincs order and lincs iter? /Erik Thanks for your suggestion, I tried without success and I also tried shake. But this is also rather fighting the symptoms than the cause... And amber simulations in vacuum do work fine... My personal guess was that another parameter in my mdp file was not compatible with the amber force field, but I could not figure out which one. I also tried different settings, e.g. the one I found on the acpypi wiki. servaas skrev: Message: 6 Date: Tue, 01 Dec 2009 07:38:29 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] amber force field in Gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b142d45.5050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed servaas wrote: Hello, I tried using the amber force field in GROMACS. I proceeded as follows: Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine. When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent): integrator = md dt = 0.002 nsteps = 25 nstcomm = 1 ;output nstxout = 1 nstvout = 1 nstfout = 0 nstlog= 500 nstenergy = 1 nstlist = 10 ns_type = grid rlist= 1.2 coulombtype = PME rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.2 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-5 ;constraints constraints = all-bonds ; temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps = system ref_t = 300 pcoupl = no I get LINCS errors and eventually a crash. Now I tried running the same simulation with the same force field parameters in amber and everything was fine. I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here) that I created in tleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'. The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions? Strange also that double precision seems to work just fine When switching precision, are the starting configurations different? What are the actual command lines in your procedures? It is the exact same structure, when I look at the trajectory I see the O3'-H rotate towards the O4' in the single precision trajectory they come too close and clash. In the double precision trajectory the O3'-H also rotates towards O4' but they do not come so close... I did not include the command lines for amber and RED, please let me know if they are relevant to you. So first I use RED to determine the charges of different fragments of my molecule. The result are several mol2 files, I use tleap to combine this mol2 file with parts of existing amber fragments. I save an amber top and amber crd file. I convert this with amb2gmx or with acpypi (tried both same result in the simulation). ./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro or python acpypi.py -x ad_test.crd -p ad_test.top -o gmx -b gro Then I add a box in gromacs: editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro I run a minimization: grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr mdrun -deffnm em (Also tried putting a position restraint step in between, did not resolve the problem) grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr mdrun -deffnm md Extra remarks: Simulation in vacuum is not realistic and the FF is not made for this but I also tried running it with counter ions and water, same result. In amber I can simulate the exact same molecule in vacuum, with same parameters without any problems. The exact same problem occurs if I start with a small natural nucleic acid sequence (3*DA), so 100% amber FF parameters (but created in amber
[gmx-users] Re: amber force field in Gromacs
Dear Servaas, I've been following your thread. I am the developer of acpypi and thanks for giving a try. So, as you may already know, you are trying acpypi as amb2gmx.pl so far, but you also seemed to have read acpypi wikis and realise that acpypi can help you to generate the whole topology for a ligand. However, AFAIU you have only regular NA and not modified ones neither ligands, right? But then why are you using RED? I understand your approach about using tleap to create your whole system and then convert it to GMX. It should work at first but it is clearly not as you reported. So, here goes some of my recommendations: 1) GMX is vacuum is unrealistic and prone for errors. There's no GB implementation as far as I know. 2) Have you try to use pdb2gmx to generate your files from your pdb directly to GMX? 3) When you say that gmx double precision works, is your system in vacuum or with solvent? 4) if using tleap, create your system with solvent and ions and then use acpypi to convert to gmx. The use of amb2gmx or acpypi is to give you a system to be run immediately in gromacs doing just a grompp and mdrun. Using editconf will change the parameters of your box and it may have serious implications besides that in amber we don't have dodecahedron, so if doing what you're doing then you're not replicating the conditions you have in amber with those in gmx (although it puzzles me that gmx double works, with the commands you gave in gmx?). I would ask you to give more details and even a detailed step by step of commands of what you're doing including tleap. Regards, Alan On Tue, Dec 1, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote: Thanks for your suggestion, I tried without success and I also tried shake. But this is also rather fighting the symptoms than the cause... And amber simulations in vacuum do work fine... My personal guess was that another parameter in my mdp file was not compatible with the amber force field, but I could not figure out which one. I also tried different settings, e.g. the one I found on the acpypi wiki. -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php